Microbiomes of fish species can provide researchers with an abundance of information on the condition of fishes in regards to their environment. We’re interested in the differences in the intestinal microbial diversity of native fish species within the Colorado river. The Colorado river as we know it is an extremely diverse ecosystem with there currently being monitoring of the rare species present and the rapid environmental changes occurring like drought and climate change. Fish that have abnormal gut microbiomes may be consuming new or different food sources or have been subject to environmental contamination. Diets also delineate information about the condition of the habitat and the general health of the fish by providing insights into food sources. When examining the gut contents of species within unique environments like the Grand Canyon, microbiomes provide vital information on their hosts and the function of the ecosystem at large.
We extracted DNA from 56 mainstem and 58 tributary water samples along with fish fecal samples from 20 rainbow trout, 77 humpback chub and 255 flannelmouth suckers from the Colorado River located in the Grand Canyon. Fish were caught using hoop nets and information on their length and weight was also taken with the samples being collected in April 2022-2024. DNA was extracted using Qiagen Powersoil kits and sequenced using the Earth Microbiome Project 16s metabarcoding procedure.
Utilizing the sequenced DNA, we were able to calculate overall microbial richness of the samples and identify patterns of the most common microbial taxa listed. We found that the flannelmouth suckers (FMS, Catostomus latipinnis) had a significantly higher microbial richness per sample than the humpback chub (HBC, Gila cypha) with FMS having a mean richness of around 120 unique taxa and the HBC averaging at about 90 unique taxa present. We found that Entrobactereales, a common order of gut bacteria found in both species, were significantly more common in humpback chub than flannelmouth suckers. We also described changing trends in microbiomes across sampling years. These differences can assist us in bettering policy and care for the landmark to maintain it for future generations.